`mach2.MACH`

Solver object for MACH2

Class Constructor

mach2.MACH(
    phylogeny,
    primary_site=None,
    suboptimal_mode=False,
    seeding_site=False,
    specify_migration_comigration=None,
    possible_migration_list=None,
    clones_observed=None)

Parameters

phylogeny (Phylogeny): The tree with unlabeled internal nodes

Optional

primary_site (str): The anatomical location of the primary site.
suboptimal_mode (bool): Return suboptimal solutions as well.
seeding_site (bool): TODO
specify_migration_comigration (TODO): TODO
possible_migration_list (list): Array of length-2 arrays containing strings representing anatomical locations. Constrains possible migrations in solution space.
clones_observed (TODO): TODO

Methods

`add_polytomy_resolution_compatibility_constraints()`

Updates the constraints for polytomy resolution.

`add_constraints_for_z()`

TODO

`add_constraints_for_z_b_R_suboptimal()`

TODO

`add_constraints_for_q()`

TODO

`add_constraints_for_q_suboptimal()`

TODO

`add_constraints_binary()`

TODO

`add_primary_site_constraints(primary_site)`

Dynamically the constraint on primary tumor location.

Parameters

primary_site (str): Location of the primary tumor

`add_contraints_specifying_mig_comig()`

TODO

`solve(solver, nSolutions, logfile='', n_threads=0, raw=False)`

Solves the Parsimonious Migration History problem with Tree Resolution (PMH-TR) given the conditions specified in the class parameters.

Parameters

solver (str): ILP solver to use. We currently only support Gurobi ("gurobi"), and hope to add support for more ILP solvers in the future.
nSolutions (int): The number of solutions returned by MACH2
n_threads (int): Number of threads to run in parallel.
raw (bool/object): Raw data describing the solution set. If the user just needs to cast the solution data, then raw data can be passed in without necessarily running MACH2